Merge branch 'master' of git://github.com/pezmaster31/bamtools

[bamtools.git] / src / api / BamReader.cpp

diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp
index 874cd839925a6963626728c6cab136f3075f2025..93a991bd77f942becb85fa505dba8b6334a15be1 100644 (file)
--- a/src/api/BamReader.cpp
+++ b/src/api/BamReader.cpp
@@ -3,7 +3,7 @@
 // Marth Lab, Department of Biology, Boston College\r
 // All rights reserved.\r
 // ---------------------------------------------------------------------------\r
-// Last modified: 3 September 2010 (DB)\r
+// Last modified: 7 September 2010 (DB)\r
 // ---------------------------------------------------------------------------\r
 // Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
 // Institute.\r
@@ -282,7 +282,7 @@ bool BamReader::BamReaderPrivate::BuildCharData(BamAlignment& bAlignment) {
                     break;  // for 'H' - hard clip, do nothing to AlignedBases, move to next op\r
                     \r
                 default:\r
-                    printf("ERROR: Invalid Cigar op type\n"); // shouldn't get here\r
+                    fprintf(stderr, "ERROR: Invalid Cigar op type\n"); // shouldn't get here\r
                     exit(1);\r
             }\r
         }\r
@@ -330,7 +330,7 @@ bool BamReader::BamReaderPrivate::BuildCharData(BamAlignment& bAlignment) {
                     break;\r
                 \r
                 default : \r
-                    printf("ERROR: Invalid tag value type\n"); // shouldn't get here\r
+                    fprintf(stderr, "ERROR: Invalid tag value type\n"); // shouldn't get here\r
                     exit(1);\r
             }\r
         }\r
@@ -383,7 +383,7 @@ bool BamReader::BamReaderPrivate::CreateIndex(bool useStandardIndex) {
     \r
     // create index based on type requested\r
     if ( useStandardIndex ) \r
-        NewIndex = new BamDefaultIndex(&mBGZF, Parent, IsBigEndian);\r
+        NewIndex = new BamStandardIndex(&mBGZF, Parent, IsBigEndian);\r
     // create BamTools 'custom' index\r
     else\r
         NewIndex = new BamToolsIndex(&mBGZF, Parent, IsBigEndian);\r
@@ -520,7 +520,7 @@ bool BamReader::BamReaderPrivate::Jump(int refID, int position) {
     // determine possible offsets\r
     vector<int64_t> offsets;\r
     if ( !NewIndex->GetOffsets(Region, IsRightBoundSpecified, offsets) ) {\r
-        printf("ERROR: Could not jump: unable to calculate offset for specified region.\n");\r
+        fprintf(stderr, "ERROR: Could not jump: unable to calculate offset for specified region.\n");\r
         return false;\r
     }\r
       \r
@@ -550,12 +550,12 @@ void BamReader::BamReaderPrivate::LoadHeaderData(void) {
     // check to see if proper BAM header\r
     char buffer[4];\r
     if (mBGZF.Read(buffer, 4) != 4) {\r
-        printf("Could not read header type\n");\r
+        fprintf(stderr, "Could not read header type\n");\r
         exit(1);\r
     }\r
 \r
     if (strncmp(buffer, "BAM\001", 4)) {\r
-        printf("wrong header type!\n");\r
+        fprintf(stderr, "wrong header type!\n");\r
         exit(1);\r
     }\r
 \r